WO2020242765A1 - Peptides modifiés à l'échelle mésométrique et procédés de sélection - Google Patents

Peptides modifiés à l'échelle mésométrique et procédés de sélection Download PDF

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Publication number
WO2020242765A1
WO2020242765A1 PCT/US2020/032715 US2020032715W WO2020242765A1 WO 2020242765 A1 WO2020242765 A1 WO 2020242765A1 US 2020032715 W US2020032715 W US 2020032715W WO 2020242765 A1 WO2020242765 A1 WO 2020242765A1
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WIPO (PCT)
Prior art keywords
constraints
derived
reference target
engineered peptide
peptide
Prior art date
Application number
PCT/US2020/032715
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English (en)
Inventor
Matthew P. Greving
Kevin Eduard HAUSER
Andrew Morin
Jordan R. WILLIS
Original Assignee
Rubryc Therapeutics, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Publication date
Application filed by Rubryc Therapeutics, Inc. filed Critical Rubryc Therapeutics, Inc.
Priority to CA3142227A priority Critical patent/CA3142227A1/fr
Priority to EP20813167.2A priority patent/EP3977117A4/fr
Priority to CN202080050892.XA priority patent/CN114585918A/zh
Priority to JP2021570755A priority patent/JP2022535511A/ja
Priority to KR1020217043265A priority patent/KR20220041784A/ko
Publication of WO2020242765A1 publication Critical patent/WO2020242765A1/fr
Priority to US17/537,215 priority patent/US20220081472A1/en

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    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/001Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6845Methods of identifying protein-protein interactions in protein mixtures
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00Machine learning
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00Machine learning
    • G06N20/10Machine learning using kernel methods, e.g. support vector machines [SVM]
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00Machine learning
    • G06N20/20Ensemble learning
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00Computing arrangements using knowledge-based models
    • G06N5/01Dynamic search techniques; Heuristics; Dynamic trees; Branch-and-bound
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00Computing arrangements using knowledge-based models
    • G06N5/04Inference or reasoning models
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/20Protein or domain folding
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/30Dynamic-time models
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K1/00General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/10General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length using coupling agents
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • G06N3/044Recurrent networks, e.g. Hopfield networks
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/04Architecture, e.g. interconnection topology
    • G06N3/045Combinations of networks
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02ATECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Software Systems (AREA)
  • Data Mining & Analysis (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Organic Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medicinal Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Biomedical Technology (AREA)
  • Evolutionary Biology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Immunology (AREA)
  • Computational Linguistics (AREA)
  • Genetics & Genomics (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Physiology (AREA)
  • Analytical Chemistry (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Pathology (AREA)

Abstract

L'invention concerne des peptides modifiés qui comprennent une combinaison de contraintes topologiques associées à l'espace, au moins une contrainte étant dérivée d'une cible de référence, et des procédés de sélection desdits peptides modifiés. L'invention concerne en outre des procédés d'utilisation des peptides modifiés, comprenant en tant que molécules de sélection positive et/ou négative dans des procédés de criblage une bibliothèque de molécules de liaison.
PCT/US2020/032715 2019-05-31 2020-05-13 Peptides modifiés à l'échelle mésométrique et procédés de sélection WO2020242765A1 (fr)

Priority Applications (6)

Application Number Priority Date Filing Date Title
CA3142227A CA3142227A1 (fr) 2019-05-31 2020-05-13 Peptides modifies a l'echelle mesometrique et procedes de selection
EP20813167.2A EP3977117A4 (fr) 2019-05-31 2020-05-13 Peptides modifiés à l'échelle mésométrique et procédés de sélection
CN202080050892.XA CN114585918A (zh) 2019-05-31 2020-05-13 中尺度工程化肽和选择方法
JP2021570755A JP2022535511A (ja) 2019-05-31 2020-05-13 メソスケール操作されたペプチドおよび選択方法
KR1020217043265A KR20220041784A (ko) 2019-05-31 2020-05-13 메소 스케일 조작된 펩티드 및 선택 방법
US17/537,215 US20220081472A1 (en) 2019-05-31 2021-11-29 Meso-scale engineered peptides and methods of selecting

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201962855767P 2019-05-31 2019-05-31
US62/855,767 2019-05-31

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US17/537,215 Continuation US20220081472A1 (en) 2019-05-31 2021-11-29 Meso-scale engineered peptides and methods of selecting

Publications (1)

Publication Number Publication Date
WO2020242765A1 true WO2020242765A1 (fr) 2020-12-03

Family

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Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2020/032724 WO2020242766A1 (fr) 2019-05-31 2020-05-13 Appareil à base d'apprentissage automatique pour la modification de peptides à l'échelle méso et procédés et système pour celui-ci
PCT/US2020/032715 WO2020242765A1 (fr) 2019-05-31 2020-05-13 Peptides modifiés à l'échelle mésométrique et procédés de sélection

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2020/032724 WO2020242766A1 (fr) 2019-05-31 2020-05-13 Appareil à base d'apprentissage automatique pour la modification de peptides à l'échelle méso et procédés et système pour celui-ci

Country Status (7)

Country Link
US (3) US11545238B2 (fr)
EP (2) EP3976083A4 (fr)
JP (2) JP2022535511A (fr)
KR (2) KR20220041784A (fr)
CN (2) CN114585918A (fr)
CA (2) CA3142339A1 (fr)
WO (2) WO2020242766A1 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115512763A (zh) * 2022-09-06 2022-12-23 北京百度网讯科技有限公司 多肽序列的生成方法、多肽生成模型的训练方法和装置

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117980995A (zh) * 2021-05-21 2024-05-03 蛋白胨有限公司 多肽结构的时空确定
CN114065620B (zh) * 2021-11-11 2022-06-03 四川大学 基于像素图表征和cnn的可解释性分子动力学轨迹分析方法
WO2023215887A1 (fr) * 2022-05-06 2023-11-09 Dyno Therapeutics, Inc. Système et procédés de prédiction de caractéristiques de séquences biologiques
CN115881220B (zh) * 2023-02-15 2023-06-06 北京深势科技有限公司 一种抗体结构预测的处理方法和装置
CN116913395B (zh) * 2023-09-13 2023-11-28 青岛虹竹生物科技有限公司 一种构建小分子肽数据库的数字化方法

Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002064734A2 (fr) * 2000-12-19 2002-08-22 Palatin Technologies, Inc. Identification de sites de repliement specifiques a la cible dans des peptides et des proteines
US20060020396A1 (en) * 2002-09-09 2006-01-26 Rene Gantier Rational directed protein evolution using two-dimensional rational mutagenesis scanning
US20070016380A1 (en) * 1998-10-21 2007-01-18 The University Of Queensland Protein engineering
US8374828B1 (en) * 2007-12-24 2013-02-12 The University Of North Carolina At Charlotte Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function
US20130090265A1 (en) 2011-10-11 2013-04-11 Biolauncher Ltd. Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices
WO2016005969A1 (fr) * 2014-07-07 2016-01-14 Yeda Research And Development Co. Ltd. Procédé de conception assistée par ordinateur de protéines
WO2020102603A1 (fr) * 2018-11-14 2020-05-22 Rubryc Therapeutics, Inc. Polypeptides cd25 génétiquement modifiés et leurs utilisations

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE60015564T2 (de) * 1999-08-02 2005-12-22 Synt:Em (S.A.) Berechnungsmethoden zur herstellung von molekularen mimetika
EP1482434A3 (fr) * 2001-08-10 2006-07-26 Xencor, Inc. Automatisation de la conception des protéines pour l'élaboration des bibliothèques de protéines
US20070192033A1 (en) 2006-02-16 2007-08-16 Microsoft Corporation Molecular interaction predictors
US8050870B2 (en) 2007-01-12 2011-11-01 Microsoft Corporation Identifying associations using graphical models
AU2011305371B2 (en) * 2010-09-21 2015-05-21 Massachusetts Institute Of Technology Human-adapted HA polypeptides, vaccines, and influenza treatment
WO2014022817A2 (fr) 2012-08-03 2014-02-06 Novartis Ag Procédés pour identifier des restes acide aminé impliqués dans une liaison macromoléculaire et leurs utilisations
US10155031B2 (en) * 2012-11-28 2018-12-18 Biontech Rna Pharmaceuticals Gmbh Individualized vaccines for cancer
CN107921090A (zh) 2015-04-06 2018-04-17 苏伯多曼有限责任公司 含有从头结合结构域的多肽及其用途
US20180068054A1 (en) * 2016-09-06 2018-03-08 University Of Washington Hyperstable Constrained Peptides and Their Design
EP3568782A1 (fr) 2017-01-13 2019-11-20 Massachusetts Institute Of Technology Conception d'anticorps basée sur l'apprentissage automatique
US20210284695A1 (en) * 2017-04-28 2021-09-16 University Of Washington Folded and protease-resistant polypeptides
MX2021007556A (es) 2018-12-21 2021-09-10 Biontech Us Inc Método y sistemas de predicción de epítopos específicos de hla de clase ii y caracterización de células t cd4+.

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070016380A1 (en) * 1998-10-21 2007-01-18 The University Of Queensland Protein engineering
WO2002064734A2 (fr) * 2000-12-19 2002-08-22 Palatin Technologies, Inc. Identification de sites de repliement specifiques a la cible dans des peptides et des proteines
US20060020396A1 (en) * 2002-09-09 2006-01-26 Rene Gantier Rational directed protein evolution using two-dimensional rational mutagenesis scanning
US8374828B1 (en) * 2007-12-24 2013-02-12 The University Of North Carolina At Charlotte Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function
US20130090265A1 (en) 2011-10-11 2013-04-11 Biolauncher Ltd. Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices
WO2016005969A1 (fr) * 2014-07-07 2016-01-14 Yeda Research And Development Co. Ltd. Procédé de conception assistée par ordinateur de protéines
WO2020102603A1 (fr) * 2018-11-14 2020-05-22 Rubryc Therapeutics, Inc. Polypeptides cd25 génétiquement modifiés et leurs utilisations

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP3977117A4

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115512763A (zh) * 2022-09-06 2022-12-23 北京百度网讯科技有限公司 多肽序列的生成方法、多肽生成模型的训练方法和装置
CN115512763B (zh) * 2022-09-06 2023-10-24 北京百度网讯科技有限公司 多肽序列的生成方法、多肽生成模型的训练方法和装置

Also Published As

Publication number Publication date
US11545238B2 (en) 2023-01-03
CN114585918A (zh) 2022-06-03
CA3142227A1 (fr) 2020-12-03
CA3142339A1 (fr) 2020-12-03
US20210166788A1 (en) 2021-06-03
KR20220039659A (ko) 2022-03-29
WO2020242766A1 (fr) 2020-12-03
US20220081472A1 (en) 2022-03-17
EP3976083A4 (fr) 2023-07-12
EP3977117A4 (fr) 2023-08-16
EP3976083A1 (fr) 2022-04-06
US20230095685A1 (en) 2023-03-30
CN114401734A (zh) 2022-04-26
KR20220041784A (ko) 2022-04-01
EP3977117A1 (fr) 2022-04-06
JP2022535511A (ja) 2022-08-09
JP2022535769A (ja) 2022-08-10

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